removed @benchmark from test

Author: behinger

Project.toml

@@ -1,7 +1,7 @@
 name = "ClusterDepth"
 uuid = "c8d8bbfa-f476-4995-adff-2987f04015d1"
 authors = ["Benedikt V. Ehinger", "Maanik Marathe"]
-version = "0.2.4"
+version = "0.2.5"
 
 [deps]
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

src/cluster.jl

@@ -26,23 +26,23 @@ function clusterdepth(
     rng,
     data::AbstractArray;
     τ=2.3,
-    stat_type = :onesample_ttest,
-    perm_type = :sign,
-    side_type = :abs,
-    nperm = 5000,
-    pval_type = :troendle,
-    (statfun!) = nothing,
-    statfun = nothing,
-	permfun = nothing,
+    stat_type=:onesample_ttest,
+    perm_type=:sign,
+    side_type=:abs,
+    nperm=5000,
+    pval_type=:troendle,
+    (statfun!)=nothing,
+    statfun=nothing,
+    permfun=nothing,
 )
     if stat_type == :onesample_ttest && isnothing(statfun!) && isnothing(statfun)
         statfun! = studentt!
         statfun = studentt
     end
     if perm_type == :sign
-		if  isnothing(permfun)
-        permfun = sign_permute!
-		end
+        if isnothing(permfun)
+            permfun = sign_permute!
+        end
     end
     if side_type == :abs
         sidefun = abs
@@ -51,11 +51,15 @@ function clusterdepth(
     elseif side_type == :negative
         sidefun = x -> -x
     elseif side_type == :positive
-        sidefun = nothing # the default :)
+        sidefun = x -> x # the default :)
     else
         @assert isnothing(side_type) "unknown side_type ($side_type) specified. Check your spelling and ?clusterdepth"
     end
+    data_obs = sidefun.(statfun(data))
 
+    if any(data_obs[:, 1] .> τ) || any(data_obs[:, end] .> τ)
+        @warn "Your data shows a cluster that starts before the first sample, or ends after the last sample. There exists a fundamental limit in the ClusterDepth method, that the clusterdepth for such a cluster cannot be determined. Maybe you can extend the epoch to include more samples?"
+    end
     cdmTuple = perm_clusterdepths_both(
         rng,
         data,
@@ -67,7 +71,7 @@ function clusterdepth(
         sidefun=sidefun,
     )
 
-    return pvals(statfun(data), cdmTuple, τ; type=pval_type)
+    return pvals(data_obs, cdmTuple, τ; type=pval_type)
 end
 
 
@@ -109,9 +113,9 @@ function perm_clusterdepths_both(
             # inplace!
             statfun!(d0, d_perm)
         end
-        if !isnothing(sidefun)
-            d0 .= sidefun.(d0)
-        end
+
+        d0 .= sidefun.(d0)
+
         # get clusterdepth
         (fromTo, head, tail) = calc_clusterdepth(d0, τ)
 

src/utils.jl

@@ -90,7 +90,7 @@ my_statfun = x->studentt_unpaired(x,grp)
 ```
 
 """
-function studentt_unpaired(x::AbstractArray, group)
+function studentt_unpaired(x, group)
     x_reshaped = reshape(x, :, size(x, ndims(x)))
     x₁ = x_reshaped[:, group]
     x₂ = x_reshaped[:, .!group]

test/cluster.jl

@@ -16,14 +16,52 @@
     )
     @test s == [3, 5]
     @test l == [0, 1]
+
+    s, l = ClusterDepth.cluster(
+        [4.0, 0.0, 10.0, 0.0, 3.0, 4.0, 0, 4.0, 4.0] .> 0.9,
+    )
 end
 
 @testset "Tests for 2D data" begin
     data = randn(StableRNG(1), 4, 5)
-    @show ClusterDepth.calc_clusterdepth(data, 0)
+    res = ClusterDepth.clusterdepth(data; τ=0.4)
+    @test size(res) == (4,)
 end
 
 @testset "Tests for 3D data" begin
     data = randn(StableRNG(1), 3, 20, 5)
-    @show ClusterDepth.clusterdepth(data; τ=0.4, nperm=5)
+    res = ClusterDepth.clusterdepth(data; τ=0.4, nperm=5)
+    @test size(res) == (3, 20)
 end
+@testset "Test sidefun" begin
+    data = randn(StableRNG(1), 23, 20)
+    data[3:8, :] .+= 3
+    data[12:17, :] .-= 3
+    res = ClusterDepth.clusterdepth(data; τ=0.4, nperm=5)
+    res_negated = ClusterDepth.clusterdepth(.-data; τ=0.4, nperm=5)
+    @test res ≈ res_negated # should be same if side_type=:abs
+
+
+    # testing the default is abs
+    res_abs = ClusterDepth.clusterdepth(data; τ=0.4, nperm=5, side_type=:abs)
+    @test res ≈ res_abs
+
+
+    res_pos = ClusterDepth.clusterdepth(data; τ=0.4, nperm=5, side_type=:positive)
+    @test all(res_pos[3:8] .< 0.8)
+    res_neg = ClusterDepth.clusterdepth(data; τ=0.4, nperm=5, side_type=:negative)
+    @test all(res_neg[12:17] .< 0.8)
+
+
+end
+@testset "Test warning clusterbegin/end" begin
+
+    # test the warning that clusters must not begin/end with a potentially significant cluster
+    data = randn(StableRNG(1), 23, 20)
+    data[1:5, :] .+= 3
+    @test_warn x -> occursin("Your data shows a cluster", x) Warning ClusterDepth.clusterdepth(data; τ=0.4, nperm=5)
+    data = randn(StableRNG(1), 23, 20)
+    data[23, :] .-= 3
+    @test_warn x -> occursin("Your data shows a cluster", x) Warning ClusterDepth.clusterdepth(data; τ=0.4, nperm=5)
+
+end

test/utils.jl

@@ -67,9 +67,11 @@ end
     x2 = _x[:, :, 2]
     x = hcat(x1, x2)
     group = repeat([false, true], inner=size(x1, 2))
+
     t = ClusterDepth.studentt_unpaired(x, group)
 
 
+
     t_true = [HypothesisTests.UnequalVarianceTTest(r[group], r[.!group]).t for r in eachrow(x)]
     @test all(t .≈ t_true)
     @test length(t) == 10000
@@ -81,5 +83,5 @@ end
     x = cat(x1, x2, dims=3)
     group = repeat([false, true], inner=size(x1, 3))
     t = ClusterDepth.studentt_unpaired(x, group .== 1)
-    @test size(t) == (1000, 50)
+    @test size(t) == (10000, 50)
 end